Technical Abstract:
Salmonella is a foodborne pathogen persistently present in some cattle herds. Some animals are carriers while other animals, despite constant exposure to the pathogen, appear resistant to colonization. One explanation for this phenomenon may be that the extant microbiota of some animals effectively excludes Salmonella from the intestinal tract, a concept known as competitive exclusion. It is known from culture and molecular analyses of the intestinal microbiota, from species ranging from humans to termites, that these communities are highly diverse and individuals host unique consortia. The objective of this work was to identify differences in the fecal microbiota from cohabiting cattle with and without a history of shedding Salmonella. To achieve this objective we used an array-based approach that uses 16S rDNA gene clone libraries to analyze microbial composition. This approach designated as Oligonucleotide Fingerprinting of Ribosomal Genes (OFRG) was performed using DNA from 19 fecal samples from Salmonella -positive (12 samples) and Salmonella -negative (7 samples) cattle. Based on fingerprint analysis of 1442 rDNA clones, the bacteria belonged to the following phyla: Firmicutes (49%), Proteobacteria (16%), Bacteroidetes (34%), Deferribacteria (0.2%), and unknown (1%). Greedy clique partitioning fingerprint clustering indicated that operational taxonomic units were primarily composed of clones from both Salmonella negative and positive animals. However, three clusters primarily consisted of samples from the Salmonella negative cattle (42 clones total). Sequence analysis of the three clusters revealed they were comprised of Firmicutes and Bacteriodetes. More specifically the genera Clostridium, Ruminococcus, Papillobacter, Treponema, Bacteroides, and Prevotella were identified within these three clusters. In this study we show the microbial diversity in the intestinal tract of cattle that shed Salmonella compared to cattle that have no history of shedding Salmonella. These data could indicate a role for anaerobic species in the competitive exclusion of Salmonella from the cattle intestinal tract.